Genetic characterization of blaNDM-1-positive Klebsiella quasipneumoniae subsp. similipneumoniae from a human carrier

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Abstract Carbepenem-resistant Klebsiella quasipneumoniae have increasingly been reported across many regions, yet data on the carbapenemase-producing isolates remain scarce. This study aimed to characterize the bla NDM-1 -positive Klebsiella sp. strain M42D recovered from a human carrier in Thailand. Strain M42D exhibited high-level resistance to carbapenems but remained susceptible to colistin. Whole genome sequencing was conducted using the Illumina and PacBio platforms. A complete genome sequence identified strain M42D as K. quasipneumoniae subsp. similipneumoniae ( Kqps ) ST334. The bla NDM-1 gene was determined to be transferable and located on the IncN2 pKquM42Da (41.2 kb). Mutations in OmpK36 and OmpK37, involved in carbapenem resistance, were observed. In silico analysis of 361 Kqps genomes showed that 9.1% of isolates, mostly from humans in Southeast Asia, carried a carbapenemase gene. Among these, bla NDM-1 was present in six isolates, with only strain M42D belonging to ST334. Core genome single-nucleotide polymorphism (SNP) analysis demonstrated that M42D clustered with other Kqps ST334 isolates with 142–186 SNP differences, suggesting that they are evolutionarily distinct strains. This study reports the first bla NDM-1 -harboring Kqps ST334 isolate, highlighting the need for further genomic surveillance of Kqps from different origins, which may help to understand the antibiotic resistance, and dissemination of Kqps within the community.

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Related topics: Antibiotic Resistance in Bacteria · Bacterial Identification and Susceptibility Testing · Nosocomial Infections in ICU